Tetramethylammonium does not universally neutralize sequence dependent DNA stability.

Effects of different concentrations of Tetramethylammonium on the thermostability of six DNA dumbbells with similar well defined sequences have been investigated. Each molecule has a 16 base pair duplex stem linked on both ends by T4 single strand loops. Only the sequence of the four central base pairs distinguishes one molecule from the next. The distinguishing central sequences are, [A-T-A-T], [T-A-T-A], [A-A-A-A], [C-G-C-G], [G-C-G-C] and [G-G-G-G] situated between the sequences: 5'-G-T-A-T-C-C-[]-G-G-A-T-A-C-3' which are the same in all molecules. Optical melting curves collected on these molecules as a function of TMA concentration over the range from 0.09 M to 4.5 M revealed there is no single concentration of TMA where all these molecules exhibit the same melting temperature.